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labsyspharm / basic-illumination

ImageJ BaSiC shading correction for use with Ashlar
MIT License
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running errors on galaxy #9

Open Xujingkk opened 1 year ago

Xujingkk commented 1 year ago

Hi mcmicro developers, I am trying to run the micmcro following galaxy, but I have difficulties with running. I have installed all tools and upload all files following "https://mcmicro.org/platforms/galaxy/". It seems can invoke the workflow but after that it reports an error in the basic illumination step, but I don’t know what the problem is and would appreciate your help.

Traceback (most recent call last): File "/home/xj/galaxy/lib/galaxy/jobs/runners/init.py", line 270, in prepare_job job_wrapper.runner_command_line = self.build_command_line( File "/home/xj/galaxy/lib/galaxy/jobs/runners/init.py", line 309, in build_command_line return build_command( File "/home/xj/galaxy/lib/galaxy/jobs/command_factory.py", line 81, in build_command handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) File "/home/xj/galaxy/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution if local_dependency_resolution and job_wrapper.dependency_shell_commands: File "/home/xj/galaxy/lib/galaxy/jobs/init.py", line 1107, in dependency_shell_commands self._dependency_shell_commands = self.tool.build_dependency_shell_commands( File "/home/xj/galaxy/lib/galaxy/tools/init.py", line 2218, in build_dependency_shell_commands return self.app.toolbox.dependency_manager.dependency_shell_commands( File "/home/xj/galaxy/lib/galaxy/tool_util/deps/init.py", line 201, in dependency_shell_commands return [ File "/home/xj/galaxy/lib/galaxy/tool_util/deps/init__.py", line 202, in dependency.shell_commands() File "/home/xj/galaxy/lib/galaxy/tool_util/deps/resolvers/conda.py", line 510, in shell_commands self.build_environment() File "/home/xj/galaxy/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment raise DependencyException("Conda dependency seemingly installed but failed to build job environment.") galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.

ArtemSokolov commented 1 year ago

@Xujingkk Is there any additional information about which Conda dependency failed? In your image.sc posts, somebody mentioned that ImageJ tools are not installed (https://forum.image.sc/t/mcmicro-failed-on-galaxy/80270/4). Did you resolve that already?

I messaged @alliecreason and Cameron Watson, who maintain the Galaxy implementation of MCMICRO to let them know that you are having problems.

Xujingkk commented 1 year ago

@ArtemSokolov Thanks for your reply. Sadly, I haven't seen any additional information about which Conda dependency failed yet. I installed galaxy under the "https://mcmicro.org/platforms/galaxy/installation.html", I don't have conda in my base environment and I was wondering if I need to install conda before installing galaxy? Besides, I'm trying to install ImageJ but haven't found a definite version in galaxy tool shed.

Xujingkk commented 1 year ago

@ArtemSokolov, I have found the exact code that reports the error, hope it is useful. image

ArtemSokolov commented 1 year ago

@Xujingkk Thanks for additional information. As I mentioned above, the Galaxy version of MCMICRO is maintained by a separate group. They will review the issue and respond here or on the imaging forum.